Methane (CH4) cycling in the Baltic Sea is studied through model simulations that incorporate the stable isotopes of CH4 (12C-CH4 and 13C-CH4) in a physical-biogeochemical model. A major uncertainty is that spatial and temporal variations in the sediment source are not well known. Furthermore, the coarse spatial resolution prevents the model from resolving shallow-water near-shore areas for which measurements indicate occurrences of considerably higher CH4 concentrations and emissions compared with the open Baltic Sea. A preliminary CH4 budget for the central Baltic Sea (the Baltic Proper) identifies benthic release as the dominant CH4 source, which is largely balanced by oxidation in the water column and to a smaller degree by outgassing. The contributions from river loads and lateral exchange with adjacent areas are of marginal importance. Simulated total CH4 emissions from the Baltic Proper correspond to an average ∼1/41.5 mmol CH4 m-2 yr-1, which can be compared to a fitted sediment source of ∼1/418 mmol CH4 m-2 yr-1. A large-scale approach is used in this study, but the parameterizations and parameters presented here could also be implemented in models of near-shore areas where CH4 concentrations and fluxes are typically substantially larger and more variable. Currently, it is not known how important local shallow-water CH4 hotspots are compared with the open water outgassing in the Baltic Sea.